BACKGROUND RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA ligase 2, a workhorse in molecular biology. Here we report the identification of a divergent RNA ligase 2 (DpRNL) from Diplonema papillatum (Diplonemea), a member of the kinetoplastids' sister group. METHODS We identified DpRNL with methods based on sensitive hidden Markov Model. Then, using homology modeling and molecular dynamics simulations, we established a three dimensional structure model of DpRNL complexed with ATP and Mg2+. RESULTS The 3D model of Diplonema was compared with available crystal structures from Trypanosoma brucei, bacteriophage T4, and two archaeans. Interaction of DpRNL with ATP is predicted to involve double π-stacking, which has not been reported before in RNA ligases. This particular contact would shift the orientation of ATP and have considerable consequences on the interaction network of amino acids in the catalytic pocket. We postulate that certain canonical amino acids assume different functional roles in DpRNL compared to structurally homologous residues in other RNA ligases 2, a reassignment indicative of constructive neutral evolution. Finally, both structure comparison and phylogenetic analysis show that DpRNL is not specifically related to RNA ligases from trypanosomes, suggesting a unique adaptation of the latter for RNA editing, after the split of diplonemids and kinetoplastids. CONCLUSION Homology modeling and molecular dynamics simulations strongly suggest that DpRNL is an RNA ligase 2. The predicted innovative reshaping of DpRNL's catalytic pocket is worthwhile to be tested experimentally.

中文翻译：

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异常RNA连接酶2的三维结构模型和预计的ATP相互作用重新连接。

背景技术RNA连接酶2是稀少的并且分散在整个生命树中。对该家族的两个成员进行了深入研究：来自寄生性锥虫（线粒体）的线粒体RNA编辑连接酶（有希望的药物靶标），以及噬菌体T4 RNA连接酶2（分子生物学中的主力军）。在这里，我们报道了从运动质体姐妹组成员乳头线虫（Diplonema papillatum）（Diplonemea）中鉴定出不同的RNA连接酶2（DpRNL）。方法我们使用基于敏感隐马尔可夫模型的方法识别了DpRNL。然后，通过同源性建模和分子动力学模拟，我们建立了与ATP和Mg2 +复合的DpRNL的三维结构模型。结果将Diplonema的3D模型与来自布氏锥虫，噬菌体T4和两个古细菌的可用晶体结构进行了比较。预测DpRNL与ATP的相互作用涉及双π堆积，这在RNA连接酶中尚无报道。这种特定的接触将改变ATP的方向，并对催化口袋中氨基酸的相互作用网络产生重大影响。我们假设某些规范性氨基酸在DpRNL中承担的功能与其他RNA连接酶2中的结构同源残基相比是不同的，这是结构性中性进化的重新分配。最后，结构比较和系统发育分析均显示，DpRNL与锥虫的RNA连接酶没有特定关系，这表明在将双倍体胶体和运动质体分开后，后者对RNA编辑具有独特的适应性。